Repo Continuity v4.4.1

Repo Continuity v4.4.1 fixes three defects that made the v4.3.0 upgrade path unusable on exactly the projects it targets.

Highlights:

• Three-way reconciliation no longer aborts the whole run when a file has two or more conflict regions. git merge-file returns the conflict count as its exit code, so any 2+ conflict file previously raised git merge-file failed: N and stopped --upgrade-apply. The longer a project has been initialized, the more certain this was to trigger.
• Genuine git merge-file failures are still raised. The check is 0 < rc < 128, because git exits 255 on error, which a plain rc > 0 would have silently misread as a conflict.
• Doctor no longer reports wiki links inside fenced blocks or inline code. Bash test syntax collides with wiki-link syntax, so a runbook quoting [[ "$rc" == "0" ]] was flagged as a broken link — a finding that could only be silenced by altering a verbatim quotation of the code under review.
• INIT.md states that the Template baseline: line in zettelkasten/AI.md is a machine-parsed contract. Rewording it leaves a repository unable to resolve its own baseline, and the failure surfaces only at the first upgrade, long after the edit. The parser error now names the expected prefix instead of only suggesting --baseline-ref.
• Adds regression coverage for both code paths and wires it into CI. The distribution smoke test only exercised initialization via --target, so --upgrade-apply and link scanning had no coverage at all, which is how these shipped.
• Registers template/INIT.md as a release-version surface so its baseline example cannot drift behind future releases.

Upgrading an initialized project: install the v4.4.1 Companion Skill, then run the three-way reconciliation as described in docs/upgrading.md. Existing projects are not modified automatically.